From 6489328ea0ed5c801a4b78805f0874d96380e9ca Mon Sep 17 00:00:00 2001 From: Tom "spot" Callaway Date: Nov 10 2010 20:19:45 +0000 Subject: forgot to update one patch --- diff --git a/EMBOSS-6.3.1-system-expat.patch b/EMBOSS-6.3.1-system-expat.patch index e964356..78fbf58 100644 --- a/EMBOSS-6.3.1-system-expat.patch +++ b/EMBOSS-6.3.1-system-expat.patch @@ -1,17 +1,7 @@ -diff -up EMBOSS-6.3.1/ajax/acd/Makefile.am.system-expat EMBOSS-6.3.1/ajax/acd/Makefile.am -diff -up EMBOSS-6.3.1/ajax/acd/Makefile.in.system-expat EMBOSS-6.3.1/ajax/acd/Makefile.in -diff -up EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am.system-expat EMBOSS-6.3.1/ajax/ajaxdb/Makefile.am -diff -up EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in.system-expat EMBOSS-6.3.1/ajax/ajaxdb/Makefile.in -diff -up EMBOSS-6.3.1/ajax/core/Makefile.am.system-expat EMBOSS-6.3.1/ajax/core/Makefile.am -diff -up EMBOSS-6.3.1/ajax/core/Makefile.in.system-expat EMBOSS-6.3.1/ajax/core/Makefile.in -diff -up EMBOSS-6.3.1/ajax/graphics/Makefile.am.system-expat EMBOSS-6.3.1/ajax/graphics/Makefile.am -diff -up EMBOSS-6.3.1/ajax/graphics/Makefile.in.system-expat EMBOSS-6.3.1/ajax/graphics/Makefile.in -diff -up EMBOSS-6.3.1/ajax/Makefile.am.system-expat EMBOSS-6.3.1/ajax/Makefile.am -diff -up EMBOSS-6.3.1/ajax/Makefile.in.system-expat EMBOSS-6.3.1/ajax/Makefile.in diff -up EMBOSS-6.3.1/configure.in.system-expat EMBOSS-6.3.1/configure.in ---- EMBOSS-6.3.1/configure.in.system-expat 2010-08-02 17:11:31.000000000 -0400 -+++ EMBOSS-6.3.1/configure.in 2010-08-02 17:12:11.831269942 -0400 -@@ -425,6 +425,7 @@ AC_ARG_ENABLE(systemlibs, +--- EMBOSS-6.3.1/configure.in.system-expat 2010-11-09 15:05:50.600682002 -0500 ++++ EMBOSS-6.3.1/configure.in 2010-11-09 15:06:25.101681999 -0500 +@@ -424,6 +424,7 @@ AC_ARG_ENABLE(systemlibs, if test "${enable_systemlibs}" = "yes" ; then have_systemlibs=yes AC_CHECK_LIB(pcre, pcre_compile) @@ -19,10 +9,19 @@ diff -up EMBOSS-6.3.1/configure.in.system-expat EMBOSS-6.3.1/configure.in fi AM_CONDITIONAL(ESYSTEMLIBS, test "$have_systemlibs" = "yes") AC_SUBST(ESYSTEMLIBS) +@@ -660,7 +661,7 @@ CHECK_THREADS + + + AC_OUTPUT([plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile +-ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile ++ajax/zlib/Makefile ajax/core/Makefile + ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile + ajax/acd/Makefile + emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile diff -up EMBOSS-6.3.1/configure.system-expat EMBOSS-6.3.1/configure ---- EMBOSS-6.3.1/configure.system-expat 2010-08-02 17:11:31.825142800 -0400 -+++ EMBOSS-6.3.1/configure 2010-08-02 17:14:33.060269076 -0400 -@@ -15339,6 +15339,51 @@ _ACEOF +--- EMBOSS-6.3.1/configure.system-expat 2010-11-09 15:05:50.603682002 -0500 ++++ EMBOSS-6.3.1/configure 2010-11-09 15:06:59.620682003 -0500 +@@ -14946,6 +14946,51 @@ _ACEOF fi @@ -74,7 +73,20 @@ diff -up EMBOSS-6.3.1/configure.system-expat EMBOSS-6.3.1/configure fi if test "$have_systemlibs" = "yes"; then ESYSTEMLIBS_TRUE= -diff -up EMBOSS-6.3.1/emboss/Makefile.am.system-expat EMBOSS-6.3.1/emboss/Makefile.am -diff -up EMBOSS-6.3.1/emboss/Makefile.in.system-expat EMBOSS-6.3.1/emboss/Makefile.in -diff -up EMBOSS-6.3.1/nucleus/Makefile.am.system-expat EMBOSS-6.3.1/nucleus/Makefile.am -diff -up EMBOSS-6.3.1/nucleus/Makefile.in.system-expat EMBOSS-6.3.1/nucleus/Makefile.in +@@ -15299,7 +15344,7 @@ fi + + + +-ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/expat/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile" ++ac_config_files="$ac_config_files plplot/Makefile plplot/lib/Makefile nucleus/Makefile ajax/Makefile ajax/zlib/Makefile ajax/core/Makefile ajax/graphics/Makefile ajax/ensembl/Makefile ajax/ajaxdb/Makefile ajax/acd/Makefile emboss/Makefile emboss/acd/Makefile test/Makefile test/data/Makefile test/embl/Makefile test/genbank/Makefile test/pir/Makefile test/swiss/Makefile test/swnew/Makefile test/testdb/Makefile emboss/data/Makefile emboss/data/AAINDEX/Makefile emboss/data/CODONS/Makefile emboss/data/REBASE/Makefile emboss/data/JASPAR_CORE/Makefile emboss/data/JASPAR_FAM/Makefile emboss/data/JASPAR_PHYLOFACTS/Makefile emboss/data/JASPAR_CNE/Makefile emboss/data/JASPAR_POLII/Makefile emboss/data/JASPAR_SPLICE/Makefile emboss/data/JASPAR_PBM/Makefile emboss/data/JASPAR_PBM_HLH/Makefile emboss/data/JASPAR_PBM_HOMEO/Makefile emboss/data/PRINTS/Makefile emboss/data/PROSITE/Makefile doc/Makefile doc/manuals/Makefile doc/tutorials/Makefile doc/programs/Makefile doc/programs/html/Makefile doc/programs/text/Makefile jemboss/Makefile jemboss/images/Makefile jemboss/lib/Makefile jemboss/lib/axis/Makefile jemboss/resources/Makefile jemboss/utils/Makefile Makefile" + + cat >confcache <<\_ACEOF + # This file is a shell script that caches the results of configure +@@ -16357,7 +16402,6 @@ do + "plplot/lib/Makefile") CONFIG_FILES="$CONFIG_FILES plplot/lib/Makefile" ;; + "nucleus/Makefile") CONFIG_FILES="$CONFIG_FILES nucleus/Makefile" ;; + "ajax/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/Makefile" ;; +- "ajax/expat/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/expat/Makefile" ;; + "ajax/zlib/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/zlib/Makefile" ;; + "ajax/core/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/core/Makefile" ;; + "ajax/graphics/Makefile") CONFIG_FILES="$CONFIG_FILES ajax/graphics/Makefile" ;;